This repo is not being developed further and has been replaced by https://github.com/anderssonlab/PRIME.
R functions for
- calling enhancers from CAGE data in the same way that was done in Andersson et al, 2014, Nature (https://doi.org/10.1038/nature12787)
- subsampling of CAGE data, e.g. for saturation analyses
- decomposition of CAGE tag clusters
- calculation of genomic background (noise) expression
- normalization across libraries versus GC content
- calculation of bias in expression coverage and expression support versus batch
The functions extend the CAGE analysis framework of CAGEfightR (https://github.com/MalteThodberg/CAGEfightR).